Into the Citadel
by Outoftheloop
Summary: The Doctor, Commander Shepard and their allies, battle old enemies in the Citadel as reality warps within it.
1. Chapter 1

\- This fan-fiction, takes place a little after the Doctor Who episode, The Caretaker, and in an AU of the Mass Effect series, where the mass relays were not destroyed in the ending where the Reapers are destroyed. -

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 **Chapter 1: The TARDIS**

Clara Oswald had just came back home after a long day at school, she threw herself onto the sofa and let out a sigh of relief. Earlier that day, Coal Hill School had a field trip to the London Zoo, and unfortunately for her, Clara had to look after two classes, as the second class's teacher had called in sick that day. The whole ordeal was taxing on Clara, one class of over-excited children was difficult enough, but two classes and throw in the fact that every child was clamoring over exotic animals, it was almost enough to cause Clara to snap.

As Clara was about to drift off into a nap, her cell phone began to ring, she sat upright on the sofa and answered the phone. "Hello?" she asked and she quickly received an answer.

"Hey, Clara. How was the zoo? I heard you had look after two classes, I bet that was a little bit of torture." The voice at the other end of the phone call was Clara's boyfriend, Danny Pink, a math teacher at Coal Hill School.

Clara said, "Hi Danny, yeah, the zoo was hectic, no one would stay still for two minutes, I thought I was going to lose a kid or two, but it's over with now. Anyways, what are you up to? I was about to take nap." Clara then leaned back on to the sofa, putting her feet on the coffee table as Danny said,

"I was wondering, if you weren't too tired, we could go out for dinner, but if you want to take a nap, how about we go out for breakfast tomorrow, since it'll be Saturday."

Clara sat back up on the sofa again and said, "We can go out for dinner, I'm not that tired. So is this going to be casual or fancy? I'll need a little time to get ready if it's…" Clara suddenly stopped talking as she heard the familiar sound of the TARDIS landing in her home. Clara then said, "Oh no, not now, I was going to get ready for a date."

Danny over heard the loud landing noise that the TARDIS made and asked in a slightly worried tone, "Clara what was that sound? Is it the Doctor?" Clara then said to Danny,

"It's him, I'm really sorry Danny, but dinner's going to have to wait, I'll tell you all about whatever happens, bye!" Clara then hung up phone and went to her bedroom, where the she presumed the TARDIS landed. The TARDIS was of course in her bedroom, squeezed between the bed and wall. Clara then entered the TARDIS and found that The Doctor was not in the main control room and so she called out for him, "Doctor? Doctor where are you?"

The Doctor then came up from the steps from the base of the TARDIS's main control in a very rushed manner and then ran right up to Clara and said, "Clara! You're here. What took you so long? Doesn't matter, I've got big news, actually, more like colossal news, monumental news. Something happened that I thought would never be able to happen, you won't believe it."

Before the Doctor could say anything else about whatever happened being a miracle, Clara stopped him and said, "Okay Doctor, stop. Breathe, calm down and tell me what happened."

The Doctor followed Clara's advice and once he had calmed down he said, "You know what the TARDIS's acronym is right?" Clara rolled her eyes in annoyance, since she thought The Doctor was stalling, still she went along with what he was doing and said,

"Yes I know what it means, Time And Relative Dimension In Space." Clara was about to ask him what any of this means, but the Doctor said,

"Right! It travels through time and space, but never dimensions, well a few times, but those were accidents and there was this one time where I left the universe. But this time, I made it to an alternate dimension and this place, it's like nothing I've ever seen before, you've got to see it for yourself." The Doctor then ran to the other side of the TARDIS control and started flipping switches and pushing buttons.

Clara was a little surprised by how excited the Doctor was about all this, he was normally quiet, reserved and rude, but this was more like how he acted in his previous incarnation, not that Clara would not mind having that fun loving time lord back for a while. Clara was curious about how the Doctor was able to accomplish this, so she asked, "So, how did you or why did you go to this new dimension?"

The Doctor, while typing in what must have been coordinates, said to Clara, "Well technically, you could call it an alternate universe, but I got there by flying the TARDIS into a wormhole and messing around with its internal structure, sending me to the same spot in an alternate universe, rather than different spot in this one. Why I did it you may ask? Well, I was bored and this was something that I've never done before, so I gave it a shot." The Doctor then flipped a lever and the TARDIS then took off shaking.

The Doctor, while hanging on to the TARDIS's console said, "Before I show you this new universe, I want to show you the wormhole and where I found it." When the TARDIS then came to a stop, Clara and the Doctor went to the doors and pulled them opened. The TARDIS was hovering over a massive pink dust cloud, he Doctor then said, "Now Clara, right below us is the Serpent Nebula, aside from a wormhole, it's nothing out of the ordinary, just an average space cloud, in this universe that is." He then closed both doors shut and ran to the monitor on the TARDIS's console, Clara following him, he then switched the monitor on and the screen showed a blue vortex.

The Doctor then said, "That is the wormhole I found and by flying into it and changing its internal structure, I came out on the other side in the exact same location, but in another universe." He switched off the monitor and fiddled around with some buttons and levers as he said, "And now, we're going to fly into it!" With a pull of one final lever, the TARDIS began to steadily shake as it flew to the wormhole, causing The Doctor and Clara to hold on the main console to maintain their balance. "Hold onto something Clara!" the Doctor yelled, "It's going to get even more rough when we travel through the wormhole!"

Clara, while trying not to fall over, went over to a nearby railing and grabbed it tightly with both of her hands and said, "Next time you redesign the TARDIS, could you put seats down here, I don't want to go flying if we hit space turbulence!" Just then, the TARDIS entered the wormhole and the shaking went from slightly unstable, to something similar to a large earthquake. Both the the Doctor and Clara held onto whatever was attached to the floor. After a minute or two of shaking, the TARDIS stood still allowing for both of them get regain their posture, Clara then asked, "Did we make it?"

The Doctor then switched the monitor back on, and grinned as he looked at the screen and said, "Yes, we've made it, look at what's on the monitor." Clara looked at the screen and saw a strange structure around the wormhole. The structure looked like two cylinders on their sides and when they came towards the wormhole they rung around it and fused at their bases and near the center for the wormhole there were two rings, spinning around it.

While Clara was impressed by the object, she did not know what it was and since the Doctor has been before, for how long she could not say, she asked him, "That's really cool, but do you know what that is?"

The Doctor then said, "I have no idea." Clara then looked at him with a confused look on her face, the Doctor said to her, "Oh, don't look at me like that, I don't know everything and this a different universe, there's bound to be countless new things to find here. Oh right, there's another thing I want to show you as well." He didn't bother turning off the monitor and rushed to the doors with Clara right behind him, the Doctor swung open both doors and looked around for a little while before he found what he was looking for in the nebula. He pointed in a slightly upward direction and said, "Look Clara! Over there in the nebula!"

Clara looked where the Doctor was pointing and her amazed to see what must have been an enormous space station, from what she could tell, floating in the pink cloud. The station looked like a five gigantic panels in a circular formation, all of them connected to a ring at their bases and in the center of the station was a giant metal sphere, connected to the rest of the station by a metal limb. Although it was still a distance away, Clara could see some lights flickering on the station, indicating that there must be people there. After getting a good look at the station, Clara then said, "That is incredible, but I don't suppose you know what that is either, right?" Clara waited for him to respond, but she didn't get anything from him, Clara turned to look at him, but the Doctor had suddenly disappeared. Clara looked back to the main console and saw him typing away while looking at the monitor, she closed the doors and walked over the main console while saying, "Doctor, what are you doing?"

The Doctor replied with, "I'm trying to log in to any kind of database or network for some information, but the TARDIS is trouble acclimating to this new universe, it will take sometime for it to work properly." The Doctor then switched off the monitor's screen, turned to face Clara and said, "While we wait for the internet to come back, why don't we explore that space station? Find out what we can on our own and take in some of the sights, what do you say?"

Before Clara could give an answer, the TARDIS suddenly suddenly shook, causing both of them to lose their balance and fall to the floor, Clara, while picking herself up said, "What was that!?"

The Doctor picked himself up and said, "Something must have hit us! The collision detectors and shields must be malfunctioning, the TARDIS should have avoided whatever hit us on it's own!" He switched the monitor back on and set to the exterior scanner, quickly locating the object that hit them and placing it on screen. At first the Doctor thought that it was a meteor or some other form of space debris that hit them, but that was not the case, the TARDIS and hit a ship, surprisingly, the ship had no signs of damage from the collision, allowing for both Clara and the Doctor to get a good look at it. The ship was smooth, sleek, futuristic, it had an overall white paint job, with black and blue stripes overlapping each other while going along the sides, the final detail that they were able to see were the words, "Normandy SR2" written on the side of the ship.

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\- Thank you for reading this chapter, please leave a review if you'd like. Also, sorry if you couldn't figure out that the Doctor and Clara, were looking at a mass relay, the Citadel and the Crucible, it is a little difficult describing some things based off their shapes alone. -


	2. Chapter 2

Chapter 2: The Normandy

The Normandy shook as if an earthquake just happened, luckily, with the ship's enhanced exterior hull, no systems were damaged, but the shaking was enough to wake up anyone sleeping on board. One of the crewmen who was abruptly awoken, was Commander Jane Shepard, she got out of bed and activated the intercom, "Joker, what was that?" she demanded and shortly after, her pilot Jeff "Joker" Moreau, responded,

"I have no idea Shep, something hit the port side thrusters, but nothing was damaged. Maybe we hit a satellite or something, whatever it was, it must have been pretty dense to shake us like that." he said.

Shepard wanting to know what hit them, said, "Scan the area around us and see what it was." she then went to go get dressed in her casual wear, a black shirt, blue jeans, sneakers, and a black leather jacket with the N7 logo on it. As soon as she was finished dressing, Joker contacted her,

"Shepard, I found what hit us." he said, sounding a bit confused with what he was seeing.

"What is it Joker?" Shepard asked.

Joker then said, "Uhh… It's a wooden box..." Joker was clearly confused and did not know what to do.

Shepard, thinking he was trying to make a joke, said, "That's really funny Joker, now tell me what really hit us."

Joker, feeling a little irritated said, "I'm not kidding you Shep, I scanned the area three times because I thought the sensors were buggy. There is a wooden box floating in space and it didn't shatter into splinters when it hit us. I must be dreaming or something because that some of the weirdest shit I've ever…" Joker didn't finish his sentence, causing Shepard to be a little worried, so she said,

"Joker? Jeff? Did something happen?" she said as she headed towards the elevator to go check up on him, just before she pressed the button to call the elevator, Joker spoke up saying,

"Okay, now I know I'm dreaming, the box just vanished into thin air, or thin space. Alright now where's EDI with cocktails and Tali taking off her helmet and her head is a smiley face balloon?" Joker was about to have a laughing fit until Shepard spoke up,

"Get a hold of yourself Joker! You're not dreaming. Now the box just disappeared? I've got to see those scanner reports myself, I'll be up there soon Joker." Shepard said, she was a bit confused like Joker, she went to her desk to grab a pistol and then went back to elevator to see Joker and check the scanner records to see if he was really telling the truth, but before she pressed the button to call the elevator, suddenly a loud voice spoke through the intercom,

"Commander, a strange blue box had just appeared in my quarters and then two humans walked out of it!" The voice other end of the intercom was Javik, the last Prothean, "I demanded that they tell me who they were, but they keep saying that they don't understand me! The older looking human had a strange device and tried to do something with my computers, I stopped him and managed to subdue them both. I suggest you come down here and sort them out, before I do." Javik said.

Shepard put her hand to forehead and thought to herself, "It's going to be a long day." She then spoke to Javik and said, "Okay, I'll be there soon, just don't hurt them Javik." Shepard then heard a different voice come from the intercom, this one sounded older, scottish and shouting from the other side of the room from the sound of it.

"Hey, hello! That sounded like english! Can you tell your friend to let us go?" The older man said, he also sounded a little angry from the sound of his voice.

Shepard then said, "You and your friend are not going anywhere, not until I prove that you're not a threat to anyone here. Just wait there, I'll be there soon enough." Shepard then deactivated the intercom connecting her to Javik, then went to the elevator and pressed the button that goes to the cargo hold.

While in the elevator, Shepard said to Joker, "Hey Joker, you were right, there was a box floating in space and when it vanished, somehow it reappeared in Javik's quarters."

Joker laughed for a few seconds before saying, "I'm not going crazy then, good. Well, I'm going to let you deal with whatever's happening, you know where to find me if you need me." The intercom then closed and Shepard was silent for the rest of the elevator ride.

It was a shorter elevator ride down to the cargo hold than it was on the old Normandy and Shepard immediately went to Javik's quarters. Shepard was surprised to see a large blue box in the corner, she then looked to the right and saw an old looking man and young girl standing against the wall with their hands up, and Javik pointing a pistol at them with one hand and holding a strange device in the other.

The old man spoke as soon as he saw Shepard and said, "Hello, I'm the Doctor and this is my friend, Clara Oswald. It's nice to meet you." The Doctor put his hand out for a handshake and tried to approach Shepard, but Javik sneered a bit and pointed the pistol at him, the Doctor then backed into the corner again with his hands back in the air and asked, "Could you tell your friend to stop pointing the gun at us?"

\- Thank you for reading this chapter, please leave a review if you'd like. -


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